<p>It seems that the author of CRCmapper.py wants to extract <code>sequence_name</code>, <code>start</code>, <code>stop</code> columns from <code>fimo.txt</code> file. But the code extract <code>motif_alt_id</code>, <code>sequence_name</code>, <code>start</code> columns. So the index of the code should be changed.</p>

<p><code>fimo.txt</code> looks like this:</p>

<pre><code>motif_id    motif_alt_id    sequence_name   start   stop    strand  score   p-value q-value matched_sequence
Transfac.V$AP1_02   AP1 NM_003046931|3|95762|152118 2332    3118    -   11.9802 6.49e-05        TGACTCA
</code></pre>

<p>In line 377-382 of the code:</p>

<p><code>line[1]</code> should be changed to <code>line[2]</code>.</p>

<pre><code>for line in fimoTable[1:]:
    source = motifDatabaseDict[line[0]]
    region = line[1].split('|')
    target = refseqToNameDict[region[0]]
    location = (region[1], int(region[2]), int(region[3]))
</code></pre>

<p>In line 391-394 of the code:</p>

<p><code>line[2]</code> should be changed to <code>line[3]</code>, <code>line[3]</code> should be changed to <code>line[4]</code>.</p>

<pre><code>    # Count unique motifs
    if (region[1], int(region[2]) + int(line[2]), int(region[2]) + int(line[3])) not in motifDictSE[source]:
        edgeCountDictSE[(source, target)] += 1
        motifDictSE[source].append((region[1], int(region[2]) + int(line[2]), int(region[2]) + int(line[3])))
</code></pre>

CC BY-SA 4.0
2018-10-25T02:54:00.713Z
2018-10-25T03:01:17.470Z
2018-10-25T03:01:17.470Z
ying
<p>This error came from the fact that  the output of the new fimo version has an additional 'motif_alt_id' column in second position. </p>

<p>CRCmapper has been modified to take this into account. You can find the updated version here: <a href="https://bitbucket.org/young_computation/crcmapper/src/master/" rel="nofollow noreferrer">https://bitbucket.org/young_computation/crcmapper/src/master/</a></p>

<p>P.S.: sorry if we missed you request user1545 and thanks for using CRCmapper!</p>

CC BY-SA 4.0
2019-07-24T17:52:19.263Z
2019-07-24T17:52:19.263Z
Violaine Saint-André
<p>I'm using <a href="https://bitbucket.org/young_computation/crcmapper/overview" rel="nofollow noreferrer">CRCmapper</a> on my data. There are several modules in the tool. I've used exactly instructed in the usage.</p>

<p>Commands used:</p>

<pre><code>python CRCmapper.py -e MB12_noEncBlack_AllEnhancers.table.txt -b MB12.bam -g HG19 -f hg19-stdChr/ -s MB12_peaks.bed -n MB12 -o MB12/
</code></pre>

<p>Here is the error I got:</p>

<pre><code>Warning: text mode turns off computation of q-values
IDENTIFY TF-TF INTERACTIONS
Traceback (most recent call last):
  File "CRCmapper.py", line 605, in &lt;module&gt;
    main()
  File "CRCmapper.py", line 593, in main
    graph = buildNetwork(projectFolder, projectName, candidateGenes, refseqToNameDict, motifConvertFile)
  File "CRCmapper.py", line 381, in buildNetwork
    target = refseqToNameDict[region[0]]
KeyError: 'AP1'
</code></pre>

<p>My expertise in python is very basic. I would be grateful if someone take a look at this error and suggest how to fix.</p>

<p>P.S. I contacted authors a long back, I didn't get any response.</p>

<p>Thank you.</p>

CC BY-SA 3.0
2017-09-28T10:55:11.780Z
It seems that the problem is within the files, are you sure that AP1 is in all your files? It could also be a bug on the software
llrs
CC BY-SA 3.0
2017-09-28T13:33:35.190Z
Yeah, it exists. For other samples, it is a different motif for different sample. It seems to be a bug in the software but I've no idea. Hope someone here will be able to understand.
user1545
CC BY-SA 3.0
2017-09-28T13:47:01.840Z
Could you paste the minimal files that reproduce the bug? Maybe you can even propose a change in the repository to fix it
llrs
CC BY-SA 3.0
2017-09-28T13:59:39.887Z
Yeah, I will prepare an example to reproduce. They haven't enabled the issue creator for their repo.
user1545
CC BY-SA 3.0
2017-09-28T14:52:05.327Z
Well you can do directly a pull request
llrs
<python><networks>
help with CRCmapper
# help with CRCmapper

(Asked by: username_0 on 2017-09-28)

I'm using CRCmapper on my data. There are several modules in the tool. I've used exactly instructed in the usage.
Commands used:
python CRCmapper.py -e MB12_noEncBlack_AllEnhancers.table.txt -b MB12.bam -g HG19 -f hg19-stdChr/ -s MB12_peaks.bed -n MB12 -o MB12/

Here is the error I got:
Warning: text mode turns off computation of q-values
IDENTIFY TF-TF INTERACTIONS
Traceback (most recent call last):
  File "CRCmapper.py", line 605, in 
    main()
  File "CRCmapper.py", line 593, in main
    graph = buildNetwork(projectFolder, projectName, candidateGenes, refseqToNameDict, motifConvertFile)
  File "CRCmapper.py", line 381, in buildNetwork
    target = refseqToNameDict[region[0]]
KeyError: 'AP1'

My expertise in python is very basic. I would be grateful if someone take a look at this error and suggest how to fix.
P.S. I contacted authors a long back, I didn't get any response.
Thank you.

**Tags:** python, networks
> **Comments:**
> **username_1**: It seems that the problem is within the files, are you sure that AP1 is in all your files? It could also be a bug on the software  
> **username_0**: Yeah, it exists. For other samples, it is a different motif for different sample. It seems to be a bug in the software but I've no idea. Hope someone here will be able to understand.  
> **username_1**: Could you paste the minimal files that reproduce the bug? Maybe you can even propose a change in the repository to fix it  
> **username_0**: Yeah, I will prepare an example to reproduce. They haven't enabled the issue creator for their repo.  
> **username_1**: Well you can do directly a pull request  

---

## 2 answers

### Answer by username_2 on 2018-10-25. Score: 2

It seems that the author of CRCmapper.py wants to extract sequence_name, start, stop columns from fimo.txt file. But the code extract motif_alt_id, sequence_name, start columns. So the index of the code should be changed.
fimo.txt looks like this:
motif_id    motif_alt_id    sequence_name   start   stop    strand  score   p-value q-value matched_sequence
Transfac.V$AP1_02   AP1 NM_003046931|3|95762|152118 2332    3118    -   11.9802 6.49e-05        TGACTCA

In line 377-382 of the code:
line[1] should be changed to line[2].
for line in fimoTable[1:]:
    source = motifDatabaseDict[line[0]]
    region = line[1].split('|')
    target = refseqToNameDict[region[0]]
    location = (region[1], int(region[2]), int(region[3]))

In line 391-394 of the code:
line[2] should be changed to line[3], line[3] should be changed to line[4].
    # Count unique motifs
    if (region[1], int(region[2]) + int(line[2]), int(region[2]) + int(line[3])) not in motifDictSE[source]:
        edgeCountDictSE[(source, target)] += 1
        motifDictSE[source].append((region[1], int(region[2]) + int(line[2]), int(region[2]) + int(line[3])))


---

### Answer by username_3 on 2019-07-24. Score: 2

This error came from the fact that the output of the new fimo version has an additional 'motif\_alt\_id' column in second position.

CRCmapper has been modified to take this into account. You can find the updated version here: <https://bitbucket.org/young_computation/crcmapper/src/master/>

P.S.: sorry if we missed you request user1545 and thanks for using CRCmapper!


---

