a strange thing about pxrms program

[FuXiaogang-KIB]

a strange thing about pxrms program

[josephwb]

You can also run Gene2 through pxlssq; if it fails there, it is almost certainly the line breaks:

pxlssq -s gene2_trimAl.txt

[FuXiaogang-KIB]

收到，谢谢！

[FuXiaogang-KIB]

List.txt
[gene1_trimAl.txt](https://github.com/FePhyFoFum/phyx/files/7223294/ge
gene2_trimAl.txt
ne1_trimAl.txt)

[josephwb]

I do not understand the problem. Why were the results incorrect? What were the results? What are the expected results? What was the command you used? Also, the upload of gene1_trimAl.txt failed.

[FuXiaogang-KIB]

gene1_trimAl.txt.txt
gene2_trimAl.txt.txt
name_List.txt
I'm sorry I wasn't clear enough.Gene1 can removes unwanted sequences normally, but other genes, such as Gene2, failed. I dont Know the reason?

[josephwb]

I'm sorry but I still do not understand what went wrong.

What is wrong with the gene2 results? What were they? What were you expecting? What command did you use?

[josephwb]

This is what I get when I examine your files:

Gene1 (original):

josephwb@Potiphar-Breen:issue$ pxlssq -s gene1_trimAl.txt 
File type: fasta
Number of sequences: 84
Is aligned: true
Sequence length: 1086
--------- Nucl TABLE ----------
Nucl        Total   Proportion
   A        19585     0.214691
   C        24941     0.273404
   G        22558     0.247281
   T        21578     0.236539
   -         2562    0.0280847
   ?            0            0
 G+C        47499     0.520685
--------- Nucl TABLE ----------

Gene1 (processed):

josephwb@Potiphar-Breen:issue$ pxrms -s gene1_trimAl.txt -f List.txt | pxlssq
File type: fasta
Number of sequences: 12
Is aligned: true
Sequence length: 1086
--------- Nucl TABLE ----------
Nucl        Total   Proportion
   A         2882     0.221148
   C         3698     0.283763
   G         3261      0.25023
   T         3182     0.244168
   -            9  0.000690608
   ?            0            0
 G+C         6959     0.533993
--------- Nucl TABLE ----------

Gene2 (original):

josephwb@Potiphar-Breen:issue$ pxlssq -s gene2_trimAl.txt 
File type: fasta
Number of sequences: 83
Is aligned: true
Sequence length: 945
--------- Nucl TABLE ----------
Nucl        Total   Proportion
   A        15583     0.198674
   C        19734     0.251597
   G        18214     0.232218
   T        15669     0.199771
   -         9235     0.117741
   ?            0            0
 G+C        37948     0.483815
--------- Nucl TABLE ----------

Gene2 (processed):

josephwb@Potiphar-Breen:issue$ pxrms -s gene2_trimAl.txt -f List.txt | pxlssq
File type: fasta
Number of sequences: 12
Is aligned: true
Sequence length: 945
--------- Nucl TABLE ----------
Nucl        Total   Proportion
   A         2294     0.202293
   C         2850     0.251323
   G         2545     0.224427
   T         2352     0.207407
   -         1299      0.11455
   ?            0            0
 G+C         5395      0.47575
--------- Nucl TABLE ----------

[josephwb]

I note that gene2_trimAl.txt seems to have Windows line breaks:

josephwb@Potiphar-Breen:issue$ file gene1_trimAl.txt 
gene1_trimAl.txt: ASCII text, with very long lines
josephwb@Potiphar-Breen:issue$ file gene2_trimAl.txt 
gene2_trimAl.txt: ASCII text, with very long lines, with CRLF line terminators

Gene2 runs fine for me (I think? I still do not know why your results are considered wrong). However, you can convert the line breaks and retry things. You will need the program dos2unix which on linuc you get with:

sudo apt-get install dos2unix

then do:

dos2unix gene2_trimAl.txt

You can check that things worked:

josephwb@Potiphar-Breen:issue$ file gene2_trimAl.txt
gene2_trimAl.txt: ASCII text, with very long lines

Finally, retry your pxrms command.

[FuXiaogang-KIB]

Dear Joseph. Thanks a lot for your meticulous reply! I will try again.

[josephwb]

Closing this since there has been no activity dum du jaroj .