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joiningdata / lollipops

Lollipop-style mutation diagrams for annotating genetic variations.
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Unable to find Arial.ttf #13

Closed tinypirate08 closed 8 years ago

tinypirate08 commented 8 years ago

Hi I tried this handy littke thing on both Mac with Yosemite 10.10.5 and on my CentOS 6.6 box. I downloaded the binaries and started with a simple command for a single gene.

I am getting the same error on both.

-bash-4.1$ ./lollipops TAF1 S1579G ERROR: Unable to find Arial.ttf - Required for accurate font sizing. Please use -f=/path/to/arial.ttf or the TTF font of your choice.

Any ideas what may be going on? Thanks

pbnjay commented 8 years ago

If somehow you don't have the Font "Arial" installed on your system, then provide the path to something else for the image generation to use for labels. Arial is part of a typical install for Yosemite so I don't know why you wouldn't have it. On your Mac, there should be a bunch of fonts you can list with ls /Library/Fonts/*.ttf but on CentOS it's probably under /usr/share/fonts/truetype/ I can't really help much with this issue other than pointing out the usage described in the error message.

For example, if you want to use another typical Mac OS X font called Andale Mono:

$ ./lollipops -f="/Library/Fonts/Andale Mono.ttf" -o test.png TAF1 S1579G
HGNC Symbol:  TAF1
Uniprot returned 46 hits for your gene symbol 'TAF1':
Entry   Entry name  Status  Gene names  Organism
P04637  P53_HUMAN   reviewed    TP53 P53    Homo sapiens (Human)
P21675  TAF1_HUMAN  reviewed    TAF1 BA2R CCG1 CCGS TAF2A   Homo sapiens (Human)
Q01105  SET_HUMAN   reviewed    SET Homo sapiens (Human)
P06400  RB_HUMAN    reviewed    RB1 Homo sapiens (Human)
Q03164  KMT2A_HUMAN reviewed    KMT2A ALL1 CXXC7 HRX HTRX MLL MLL1 TRX1 Homo sapiens (Human)
P51610  HCFC1_HUMAN reviewed    HCFC1 HCF1 HFC1 Homo sapiens (Human)
Q9Y230  RUVB2_HUMAN reviewed    RUVBL2 INO80J TIP48 TIP49B CGI-46   Homo sapiens (Human)
Q15545  TAF7_HUMAN  reviewed    TAF7 TAF2F TAFII55  Homo sapiens (Human)
Q9Y265  RUVB1_HUMAN reviewed    RUVBL1 INO80H NMP238 TIP49 TIP49A   Homo sapiens (Human)
P52655  TF2AA_HUMAN reviewed    GTF2A1 TF2A1    Homo sapiens (Human)
Q99496  RING2_HUMAN reviewed    RNF2 BAP1 DING HIPI3 RING1B Homo sapiens (Human)
Q9HCK8  CHD8_HUMAN  reviewed    CHD8 HELSNF1 KIAA1564   Homo sapiens (Human)
Q16594  TAF9_HUMAN  reviewed    TAF9 TAF2G TAFII31  Homo sapiens (Human)
P20226  TBP_HUMAN   reviewed    TBP GTF2D1 TF2D TFIID   Homo sapiens (Human)
Q8IZX4  TAF1L_HUMAN reviewed    TAF1L   Homo sapiens (Human)
Q9H7Z6  KAT8_HUMAN  reviewed    KAT8 MOF MYST1 PP7073   Homo sapiens (Human)
Q53T94  TAF1B_HUMAN reviewed    TAF1B   Homo sapiens (Human)
P61244  MAX_HUMAN   reviewed    MAX BHLHD4  Homo sapiens (Human)
Q9Y294  ASF1A_HUMAN reviewed    ASF1A CGI-98 HSPC146    Homo sapiens (Human)
P35269  T2FA_HUMAN  reviewed    GTF2F1 RAP74    Homo sapiens (Human)
P61964  WDR5_HUMAN  reviewed    WDR5 BIG3   Homo sapiens (Human)
Q8WWY3  PRP31_HUMAN reviewed    PRPF31 PRP31    Homo sapiens (Human)
P49848  TAF6_HUMAN  reviewed    TAF6 TAF2E TAFII70  Homo sapiens (Human)
Q96EZ8  MCRS1_HUMAN reviewed    MCRS1 INO80Q MSP58  Homo sapiens (Human)
Q9UBL3  ASH2L_HUMAN reviewed    ASH2L ASH2L1    Homo sapiens (Human)
Q7Z3B3  KANL1_HUMAN reviewed    KANSL1 CENP-36 KIAA1267 MSL1V1 NSL1 Homo sapiens (Human)
Q96IU4  ABHEB_HUMAN reviewed    ABHD14B CIB Homo sapiens (Human)
Q9NVP2  ASF1B_HUMAN reviewed    ASF1B   Homo sapiens (Human)
O75461  E2F6_HUMAN  reviewed    E2F6    Homo sapiens (Human)
Q9Y262  EIF3L_HUMAN reviewed    EIF3L EIF3EIP EIF3S6IP HSPC021 HSPC025 MSTP005  Homo sapiens (Human)
Q6PI98  IN80C_HUMAN reviewed    INO80C C18orf37 Homo sapiens (Human)
Q9Y4W2  LAS1L_HUMAN reviewed    LAS1L MSTP060   Homo sapiens (Human)
Q8IWI9  MGAP_HUMAN  reviewed    MGA KIAA0518 MAD5   Homo sapiens (Human)
Q8IZL8  PELP1_HUMAN reviewed    PELP1 HMX3 MNAR Homo sapiens (Human)
Q9BVI0  PHF20_HUMAN reviewed    PHF20 C20orf104 GLEA2 HCA58 NZF TZP Homo sapiens (Human)
Q15291  RBBP5_HUMAN reviewed    RBBP5 RBQ3  Homo sapiens (Human)
Q3B726  RPA43_HUMAN reviewed    TWISTNB Homo sapiens (Human)
Q9NYV6  RRN3_HUMAN  reviewed    RRN3 TIFIA  Homo sapiens (Human)
Q9H4L4  SENP3_HUMAN reviewed    SENP3 SSP3 SUSP3    Homo sapiens (Human)
Q15542  TAF5_HUMAN  reviewed    TAF5 TAF2D  Homo sapiens (Human)
Q7Z7C8  TAF8_HUMAN  reviewed    TAF8 TAFII43 TBN    Homo sapiens (Human)
Q5H9L4  TAF7L_HUMAN reviewed    TAF7L TAF2Q Homo sapiens (Human)
O00268  TAF4_HUMAN  reviewed    TAF4 TAF2C TAF2C1 TAF4A TAFII130 TAFII135   Homo sapiens (Human)
Q9NXF1  TEX10_HUMAN reviewed    TEX10 L18 Nbla10363 Homo sapiens (Human)

Selected 'Q53T94' as the best match. Use -U XXX to use another ID.

Uniprot/SwissProt Accession:  Q53T94
Drawing diagram to test.png

You probably don't want the default selection there, use the appropriate Uniprot ID (with -U XXXX):

$ ./lollipops -f="/Library/Fonts/Andale Mono.ttf" -o test.png -U P21675 S1579G   
Pfam Symbol:  TAF1_HUMAN
Drawing diagram to test.png

test

tinypirate08 commented 8 years ago

Love it! It works now. Thanks for the advice. The plot is amazing!

tinypirate08 commented 8 years ago

Hi Jeremy, One quick question. Is there a way to control the domain name labels within the colored domain bars?

What if I did not want to include the text? Looks like if I adjust image size, the text gets truncated within domains. See green and blue bars before and after.

Is there a way to adjust text size, or not to include?

I used command for TAF1.png ./lollipops -f=/Library/Fonts/Courier\ New.ttf -labels -hide-motifs -o TAF1.png -U P21675 S1579G

I used the follwing for TAF1_2.png /lollipops -f=/Library/Fonts/Courier\ New.ttf -labels -hide-motifs -w 6000-dpi 300 -o TAF1_2.png -U P21675 S1579G

I tried multiple size combinations but, there is always one domain name that is truncated.

Thanks for your input. Szabi

[cid:0B472A7B-C1D8-4ECC-9401-98B18832C28E@ad.tgen.org]

[cid:6D5F3841-C363-4D15-96B3-FEEF26D79ECC@ad.tgen.org]

Szabolcs Szelinger, Ph.D Staff Scientist Neurogenomics Division, The Translational Genomics Research Institute (TGen) 445 N. 5th Street, Phoenix AZ 85044 ph:602-343-8723 sszelinger@tgen.orgmailto:sszelinger@tgen.org

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On Feb 1, 2016, at 14:03, Jeremy Jay notifications@github.com<mailto:notifications@github.com> wrote:

Closed #13https://github.com/pbnjay/lollipops/issues/13.

— Reply to this email directly or view it on GitHubhttps://github.com/pbnjay/lollipops/issues/13#event-534824652.