Error reading fasta sequences - please check input files!

[kashiff007]

Hi thanks for this great software. While using this I am unable to start with the continuous error of "Error reading fasta sequences - please check input files!". This error also occurring with test-seqs.fas.

Full log output pasted below:

python2.7 ~/Software/flexidot/code/flexidot_v1.00.py -i ~/Software/flexidot/test-data/test-seqs.fas -g ~/Software/flexidot/test-data/example2.gff3 -G ~/Software/flexidot/test-data/gff_color.config -o Cluster_94644.txt.bed.pdf -p 2
Installing Python module: colour
	python -m pip install colour

Requirement already satisfied: colour in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (0.1.5)


Please install module colour manually
Installing Python module: colormap
	python -m pip install colormap

Installing Python module: easydev
	python -m pip install easydev

Requirement already satisfied: colormap in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (1.0.4)
Requirement already satisfied: easydev in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (0.12.0)
Requirement already satisfied: colorama in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (from easydev) (0.4.4)
Requirement already satisfied: pexpect in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (from easydev) (4.8.0)
Requirement already satisfied: colorlog in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (from easydev) (6.6.0)
Requirement already satisfied: ptyprocess>=0.5 in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (from pexpect->easydev) (0.7.0)


Please install module colormap manually
Installing Python module: biopython
	python -m pip install biopython

Requirement already satisfied: biopython in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (1.79)
Requirement already satisfied: numpy in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (from biopython) (1.21.5)


Please install module biopython manually
Installing Python module: regex
	python -m pip install regex

Requirement already satisfied: regex in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (2022.3.15)


Please install module regex manually

...reading input arguments...
fasta file #1: /Users/nawazk/Software/flexidot/test-data/test-seqs.fas
GFF file #1: /Users/nawazk/Software/flexidot/test-data/example2.gff3

----------------------------------------------------------------------

INPUT/OUTPUT OPTIONS...

Input fasta file:                                  /Users/nawazk/Software/flexidot/test-data/test-seqs.fas
Automatic fasta collection from current directory: False
Collage output:                                    True
Number of columns per page:                        4
Number of rows per page:                           5
File format:                                       png
Residue type is nucleotide:                        True


CALCULATION PARAMETERS...

Wordsize:                                          7
Plotting mode:                                     2
                                                   all-against-all 
Ambiguity handling:                                False
Reverse complement scanning:                       True
Alphabetic sorting:                                False
Prefix for output files:                           Cluster_94644.txt.bed.pdf


LCS SHADING OPTIONS (plotting_mode 'all-against-all' only)...

LCS shading:                                       False
LCS shading interval number:                       5
LCS shading reference:                             maximal LCS length
LCS shading orientation:                           forward


GRAPHIC FORMATTING...

Plot size:                                         10
Line width:                                        1
Line color:                                        black
Reverse line color:                                #009243
X label position:                                  True
Label size:                                        10
Spacing:                                           0.04
Title length (limit number of characters):         inf
Length scaling:                                    False
----------------------------------------------------------------------


==================================================

Reading GFF color configuration file
----------------------------

=> /Users/nawazk/Software/flexidot/test-data/gff_color.config

Updating GFF color configuration with custom specifications

1 feature type specifications overwritten:
	repeat_region

GFF color specification updated acc. to /Users/nawazk/Software/flexidot/test-data/gff_color.config
	misc_feat, misc_feature, spacer3, spacer2, spacer1, cds, misc, ltr_retrotransposon, ppt, tandem_repeat, target_site_duplication, intron, spacerzoom, repeat, ltr-retro, long_terminal_repeat, exon, others, orf, transposable_element, ltr, pbs, repeat_region, utr, repeat_region_rev, orf_rev, gene


==================================================

Running plotting modes 2
Error reading fasta sequences - please check input files!

Failed to load sequences

	 0.000445127487183 seconds

No image files were created!

==================================================

##################################################
##################################################

Thank you for using FlexiDot!

```

[molbio-dresden]

Dear Mr. Nawaz, I will have a look, likely over the weekend! Best wishes Tony

…

---------------------------------------------------------------------- Dr. Tony Heitkam Technische Universität Dresden Faculty of Biology Zellescher Weg 20b | Room E35 | D-01062 Dresden Tel: (+49) 0351 463 39593 Email: ***@***.*** ----------------------------------------------------------------------

________________________________ Von: Kashif Nawaz ***@***.***> Gesendet: Donnerstag, 16. Juni 2022 11:47:05 An: molbio-dresden/flexidot Cc: Subscribed Betreff: [molbio-dresden/flexidot] Error reading fasta sequences - please check input files! (Issue #14) Hi thanks for this great software. While using this I am unable to start with the continuous error of "Error reading fasta sequences - please check input files!". This error also occurring with test-seqs.fas. Full log output pasted below: `python2.7 ~/Software/flexidot/code/flexidot_v1.00.py -i ~/Software/flexidot/test-data/test-seqs.fas -g ~/Software/flexidot/test-data/example2.gff3 -G ~/Software/flexidot/test-data/gff_color.config -o Cluster_94644.txt.bed.pdf -p 2 Installing Python module: colour python -m pip install colour Requirement already satisfied: colour in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (0.1.5) Please install module colour manually Installing Python module: colormap python -m pip install colormap Installing Python module: easydev python -m pip install easydev Requirement already satisfied: colormap in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (1.0.4) Requirement already satisfied: easydev in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (0.12.0) Requirement already satisfied: colorama in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (from easydev) (0.4.4) Requirement already satisfied: pexpect in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (from easydev) (4.8.0) Requirement already satisfied: colorlog in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (from easydev) (6.6.0) Requirement already satisfied: ptyprocess>=0.5 in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (from pexpect->easydev) (0.7.0) Please install module colormap manually Installing Python module: biopython python -m pip install biopython Requirement already satisfied: biopython in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (1.79) Requirement already satisfied: numpy in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (from biopython) (1.21.5) Please install module biopython manually Installing Python module: regex python -m pip install regex Requirement already satisfied: regex in /Users/nawazk/opt/anaconda3/lib/python3.9/site-packages (2022.3.15) Please install module regex manually ...reading input arguments... fasta file #1<#1>: /Users/nawazk/Software/flexidot/test-data/test-seqs.fas GFF file #1<#1>: /Users/nawazk/Software/flexidot/test-data/example2.gff3

________________________________ INPUT/OUTPUT OPTIONS... Input fasta file: /Users/nawazk/Software/flexidot/test-data/test-seqs.fas Automatic fasta collection from current directory: False Collage output: True Number of columns per page: 4 Number of rows per page: 5 File format: png Residue type is nucleotide: True CALCULATION PARAMETERS... Wordsize: 7 Plotting mode: 2 all-against-all Ambiguity handling: False Reverse complement scanning: True Alphabetic sorting: False Prefix for output files: Cluster_94644.txt.bed.pdf LCS SHADING OPTIONS (plotting_mode 'all-against-all' only)... LCS shading: False LCS shading interval number: 5 LCS shading reference: maximal LCS length LCS shading orientation: forward GRAPHIC FORMATTING... Plot size: 10 Line width: 1 Line color: black Reverse line color: #009243 X label position: True Label size: 10 Spacing: 0.04 Title length (limit number of characters): inf Length scaling: False ================================================== Reading GFF color configuration file => /Users/nawazk/Software/flexidot/test-data/gff_color.config Updating GFF color configuration with custom specifications 1 feature type specifications overwritten: repeat_region GFF color specification updated acc. to /Users/nawazk/Software/flexidot/test-data/gff_color.config misc_feat, misc_feature, spacer3, spacer2, spacer1, cds, misc, ltr_retrotransposon, ppt, tandem_repeat, target_site_duplication, intron, spacerzoom, repeat, ltr-retro, long_terminal_repeat, exon, others, orf, transposable_element, ltr, pbs, repeat_region, utr, repeat_region_rev, orf_rev, gene ================================================== Running plotting modes 2 Error reading fasta sequences - please check input files! Failed to load sequences 0.000445127487183 seconds No image files were created! ================================================== ################################################## ################################################## Thank you for using FlexiDot! ` [image]<https://user-images.githubusercontent.com/16431099/174042793-baee0ce5-85b2-492c-ba3b-00e675513d53.png> — Reply to this email directly, view it on GitHub<#14>, or unsubscribe<https://github.com/notifications/unsubscribe-auth/AIDCCRNVHXS5A43L2EDDPB3VPLZZTANCNFSM5Y6GEOUQ>. You are receiving this because you are subscribed to this thread.Message ID: ***@***.***>

[kashiff007]

Dear Tony,

Thank you very much.

Best,
Kashif

[NAalytics]

Hello all- I am having similar issues. While the program is giving errors in a python=3.6 environment, in an environment where python=2.7 all other packages (eg, color, like it was shown above) give errors. I am unable to run the program in both of these environments. If a solution is available, please let me know.
With best wishes.
Massa